Main
Rüçhan Ekren
Currently PhD student in Bioinformatics with the expected thesis manuscript submission of Auguts 2023. Mainly working on scRNAseq data curation and its robust analysis.
Education
Bioinformatics, Genomics and Systems Biology
Paul Sabatier University of Toulouse III
Toulouse, FR
Current - 2020
- PhD Candidate
- Thesis: The Alterations of Transcriptomic Program of Natural Killer Cells in the Tumor Microenvironment of Mutiple Myeloma
Biostatics and Bioinformatics
Acibadem University
Istanbul, TR
2020 - 2017
- Master of Science
- Thesis: Transcriptomics-based Investigation of Drug Resistance Mechanisms in Triple-negative Breast Cancer Cell Lines
Molecular Biology & Genetics
Izmir Institute of Technology
Izmir, TR
2016 - 2011
- Bachelor of Science
Research Experience
Bioinformatics Analyst
GENIM - CRCT
Toulouse, FR
Current - 2020
- Establishing robust, end-to-end scRNAseq analysis pipeline with improved QC steps involved
- Being in charge of orchestration of 40 human scRNAseq samples and complementary 4 mouse scRNAseq samples
- Characterization of corresponding cell types with supervised and unsupervised approaches within cohort
- Functional analyses such as differential expression, pathway enrichment, and trajectory inference analyses
Graduate Reearch Assistant
Sezerman Bioinformatics Lab
Istanbul, TR
2020 - 2017
- Transcriptome Profile Analysis of Atherosclerosis Rabbit Model from pooled CEL-Seq2 Data
- Investigation of miRNA Activity-related Mechanisms of Drug Resistance on Breast Cancer Patients from RNA-Seq data
- Transcriptomics Analysis of Insulin-resistant Rat Model from Microarray data
Research Assistant
JLab Bioinformatics
Izmir, TR
2016 - 2015
- Processing publicly available NGS data from “1000 Genome project” to find alternative explanations of cancer causes
- Sequential mapping of genomic reads to human reference genome, bacteria genome pool and then viral genome pool
Undergraduate Researcher
Controlled in vitro Microenvironments Lab
Izmir, TR
2015 - 2012
- Optimization of PDA liposome embedded assay with breast cancer cell laden
- Fabrication of the polydiacetylene (PDA) / polyvinylalcohol (PVA) electrospun mats for cell culture applications
- Lab-on-a-chip biosensor development for rapid bacteria detection
Visiting Researcher
Internal Medicine Lab - Universitätsklinikum
Tübingen, GR
2014
- Disruptive Effect of Dietary Ethanol Stimulation on Cholangiocarcinoma cells
Teaching Experience
Omics
Acibadem University
Istanbul, TR
2020 - 2018
- Teaching Assistant
- Detailed theoretical explanation of RNA-Seq, data analysis pipeline and hands-on experience with supervised term projects
- Undergraduate class to medicine students
RNA-Seq Analysis
Acibadem University
Istanbul, TR
2018
- Within the framework of EpiSyStem (Epigenetics and System Biology of Stem cells and Reprogramming) of H2020:Marie Curie Innovative Training Networks
- Handled the organization and being teaching assistant of the workshop
- With the focus of how to leverage RNA-seq data, its analysis and practical applications
Published articles
CD137(4-1BB) Signaling Drives a TcR-Independent Exhaustion Program in CD8 T Cells
Immunity -in press-
N/A
2022
Response Assessment With Molecular Characterization of Circulating Tumor Cells and Plasma MicroRNA Profiling in Patients With Locally Advanced Breast Cancer During Neoadjuvant Chemotherapy
Clinical Breast Cancer
N/A
2020
Transcriptomics-based Investigation of Drug Resistance Mechanisms in Triple-negative Breast Cancer Cell Lines
Master Thesis
N/A
2020
Ameliorative potential of Lavandula stoechas in metabolic syndrome via multitarget interactions
Journal of Ethnopharmacology
N/A
2018
Selected Conferences and Seminars
CARe Bionformatics Workshop
Amphitheatre Oncopole
Toulouse, FR
2022
- Selected to give scientific talk about my current project by scientific commitee.
NextflowSummit 2022
Virtual Event
Barcelona, SP
2022
Network Science in Biology and Medicine (NetBioMed)
Virtual Event
Washington DC, USA
2021
- Presented scientific poster about my current project
Les Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM)
Institut Pasteur, Virtual Event
Paris, FR
2021
- Presented scientific poster about my current project
Computational Systems Biology of Cancer: Multi-omics and Machine Learning Approaches (SysBioCancer)
Institut Curie, Virtual Event
Paris, FR
2021
- Selected for doing oral presentation about my current project by scientific commitee
Combination in cancer immunotherapy resistance, from molecular aspects to clinical issues (CICOR)
Amphitheatre Oncopole
Toulouse, FR
2021
- Selected for giving a scientific talk about my current project by scientific commitee
Single-cell Genomics Day
Virtual Event
New York, USA
2021
Computational Genomics. A Hands-on Course on Machine Learning for Genomics
Virtual Bootcamp, Max Delbrück Center
Berlin, GR
2021
Extra-curriculum Activities
I also enjoy reading fictional literature, climbing, playing story-rich role-playing video games, and doing woodcarving in my free time.
International Society for Computational Biology (ISCB)
N/A
N/A
Current - 2023
- Student member
COMmitee ETudiant (COMET)
N/A
N/A
Current - 2022
- Responsible for the organization of journal clubs, workshops and other events for the students of CRCT
Société Française de Bioinformatique (SFBI)
N/A
N/A
Current - 2021
- Student member
European Association for Cancer Research (EACR)
N/A
N/A
Current - 2021
- Student member
CARe Training Council
N/A
N/A
Current - 2021
- In charge of preparing the prospective members of the Cancer, Aging, and Rejuvanation (CARe) Graduate School
Hope Foundation for Children with Cancer (KACUV)
N/A
N/A
Current - 2021
- Volunteer and donor of the foundation
Tutorship
N/A
N/A
2020 - 2018
- Volunteered tutorship for middle school kids on science and math courses
Disclaimer
This CV is made with the R packages pagedown and datadrivencv.
The public repository of this CV is hosted in here
Last updated on 2023-05-19.